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Anti-whaling group Sea Shepherd says one of its ships has been rammed by a Japanese whaling vessel.

The Bob Barker was hit by the harpoon vessel, the Yushin Maru 2, when it crossed in front of its bow in sub-Antarctic waters just before 9am (NZT), the group said.

The incident was a part of an attack by the Japanese whaling fleets' three harpoon vessels, on the Sea Shepherd ships, The Steve Irwin and The Bob Barker, which began about about 2am, Sea Shepherd said.

"The assault is an attempt to deter the Sea Shepherd ships from their current position, blocking the slipway of the Nisshin Maru, preventing the whalers from loading whales poached from the Southern Ocean Whale Sanctuary.''

During the clashes, which were continuing into afternoon, the whaling vessels had also made consecutive attempts to tangle the propellers of the Sea Shepherd ships by dragging steel cable across the bow of the conservation ships, a Sea Shepherd spokesman said.

The crew of the whaling vessels had also thrown projectiles at The Steve Irwin's small boat crew and turned water cannons on The Bob Barker's small boat crew as they attempted to cut the steel cables, he said.

The alleged attack has happened while the group was celebrating a "disastrous'' Japanese whaling operation last month as a direct result of actions taken by the Sea Shepherd ships.

"Early interception and a persistent chase has enabled the Sea Shepherd fleet to effectively suspend whaling operations and allowed the fleet to take up position and secure the slipway of the Nisshin Maru,'' the group said.